Given that the proteome reflects the physiological and pathological states of a patient, proteomics is a powerful tool for early diagnostics of diseases and monitoring of therapeutic responses. The majority of current protein assays in clinical settings are based on enzyme-linked immunosorbent assay (ELISA) immunoassays, which require high-quality antibodies and are hard to achieve with high multiplexing (e.g., greater than 10) due to the cross-reactivity of antibodies. Mass spectrometry (MS) measures the mass-to-charge ratio of charged species, and has become an enabling technology for proteomics. Aside from de novo identification of target proteins, MS has advantages over ELISA for detecting protein mutations, modification, truncations, and adductations, for example. Once combined with the liquid chromatography (LC), LC-MS enables separation, identification, characterization, and quantitation of complex mixtures of proteins and peptides. However, the penetration of MS into the in vitro diagnostics market, particularly for clinical proteomics, has remained low. Key challenges remain for an MS-based platform to achieve robustness, sensitivity, and throughput comparable to those of ELISA for analysis of small-volume biospecimens such as blood and urine.